Momocs (version 0.1-01)

pca: Calculates and plots Principal Component Analysis.

Description

Calculates and plots Principal Component Analysis usng prcomp(). Methods for plotting a single PCA, a triple PCA and deformation grids are detailed below.

Usage

pca(Nef, fac = NA,PCa = 1, PCb = 2,
	col = "black", pch = 1, lty=1, shp.nb=NA, shp.size,
	shp.col="#00000022", shp.border="black", title = "Principal Component Analysis",
	legend = TRUE, lab = FALSE, lab.txt = rownames(Nef@coeff), lab.cex = 1, lab.box = TRUE,
	ell = TRUE, r = 1, lwd = 1, zoom.x = 0.25, zoom.y = 0.3)

pca3(Nef,  fac = NA,
	col = 1:nlevels(fac), pch = 1:nlevels(fac), lty = rep(1,nlevels(fac)),
	lab = FALSE, lab.txt = rownames(Nef@coeff), lab.cex = 1, lab.box = TRUE,
	ell = 1, r = 1, lwd = 1, zoom = 1.4, legend = FALSE)

pca.tps(Nef, fac = NA, PCa = 1, PCb = 2,
		col = "black", pch = 1, ell = TRUE, zoom = 1.4, ncells = 20,
		title = "Deformations alongs PC axes")

Arguments

Nef

the Nef object

fac

the grouping factor

PCa

integer corresponding to the a^th PCA axis to plot

PCb

integer corresponding to the a^th PCA axis to plot

col

integer or character indicating the col for each group to plot

pch

integer or character indicating the pch for each groups to plot

lty

integer indicating the lty for each confidence ellipse to plot

shp.nb

integer indicating how many, if any, shapes to plot

shp.size

numeric indicating the size of these shapes

shp.col

integer or a character indicating the color of these shapes

shp.border

integer or a character indicating the border color of these shapes

title

character to add a better title to the plot

lab

logical indicating whether to plot labels for every point

lab.txt

character vector containing labels names

lab.cex

numeric indicating the cex size of these labels

lab.box

logical indicating whether to draw a border for these labs

ell

logical indicating whether to draw confidence ellipses for every group

r

numeric indicating the number of standard deviations for confidence ellipses computation

lwd

numeric indicating the lwd for the confidence ellipses

zoom

numeric used to adjust the range of the plot

zoom.x

numeric used to adjust the x-range of the plot

zoom.y

numeric used to adjust the y-range of the plot

legend

logical indicating whether to add a legend on the plot

ncells

integer indicating the number of cells for deformation grids

Examples

data(bottles.nef)
fac <- factor(rep(c("beer", "whisky"), each=20))

### pca
pca(bottles.nef)
pca(bottles.nef, fac=fac)
pca(bottles.nef, fac=fac, pch=c(4,5))
pca(bottles.nef, fac=fac, pch=c(4,5), ell=FALSE)
pca(bottles.nef, fac=fac,pch=c(4,5), lty=c(2,3))
pca(bottles.nef, pch=c(4,5), fac=fac, lty=c(2,3), col=c("dodgerblue","firebrick"))
pca(bottles.nef, fac=fac, lab=T)
pca(bottles.nef, fac=fac, lab=T, lab.cex=0.8)
pca(bottles.nef, fac=fac, lab=T, lab.box=FALSE)
pca(bottles.nef, fac=fac, lab=T, lab.txt=c(letters[1:20],LETTERS[1:20]))
pca(bottles.nef, fac=fac, r=0.5)
pca(bottles.nef, fac=fac, r=0.5, zoom.x=0.1, zoom.y=0.1)
pca(bottles.nef, PCa=2, PCb=3)
pca(bottles.nef, shp.nb=5)
pca(bottles.nef, shp.nb=5, shp.col="#FF660033", shp.border="#FF6600")

### pca3
pca3(bottles.nef)
pca3(bottles.nef, fac=fac)
pca3(bottles.nef, fac=fac, pch=c(4,5))
pca3(bottles.nef, fac=fac, pch=c(4,5), lty=c(2,3))
pca3(bottles.nef, fac=fac, pch=c(4,5), lty=c(2,3), col=c("dodgerblue","firebrick"))
pca3(bottles.nef, fac=fac, pch=c(4,5), lty=c(2,3), col=c("dodgerblue","firebrick"), legend=T)

### pca.tps
pca.tps(bottles.nef)
pca.tps(bottles.nef, fac=fac)